Facey struck with just eight minutes remaining with a calm finish for his first goal for the club.
Gillingham, who saw Ronnie Jepson depart the club last weekend, lined up in an untried 3-5-2 formation under the guidance of caretaker duo Mick Docherty and Iffy Onuora against Brighton's more familiar 4-4-2.
But after only 15 minutes of indifferent football, the Gills reverted to 4-4-2, as both sides struggled to find a cutting edge.
It took 31 minutes for either side to fashion a decent opening, Steve Lomas warming the hands of visiting keeper Michel Kuipers with a volley from distance that the Dutchman did well to palm away.
The standard of play marginally improved after the break, with Facey going close with a looping volley that landed on the roof of the net on 52 minutes.
Former Gill Bas Savage also began to enjoy greater freedom up front for the Seagulls, and his lay-off found substitute Jake Robinson whose close-range drive cannoned off Craig Armstrong's legs to safety.
Moments later, a Robinson cross appeared to strike Armstrong's arm under the noses of the travelling supporters, but the referee ignored their vociferous appeals.
Another Brighton substitute, Alex Revell, forced a smart stop out of Simon Royce in the 77th minute after Dean Cox had found him with a precise pass.
But just as Brighton appeared to be turning the screw, Nicky Southall's long throughball found Facey in space and the striker toe-poked the ball beyond Kuipers.
Brighton threw everything at Gillingham in an attempt to force an equaliser, but George O'Callaghan's late free-kick was comfortably saved by Royce.